Institute of Science Tokyo

Conditional diffusion model for 5' UTR and UTR-CDS junction design, targeting ribosome load, folding energy and codon adaptation at sampling time.

Atomic-level refinement of RNA 3D structures, using geometric attention networks to guide physics-based Monte Carlo sampling and L-BFGS optimization.

Protein sequence-structure co-embedding model placing domains, full sequences, and short segments in one 32-dimensional contrastive space.

Enzyme screening framework pairing a sequence-structure CNN classifier with CLIP-style protein-reaction retrieval to link orphan enzymes to genes.

E3 ubiquitin ligase-substrate interaction prediction from a LoRA-adapted protein language model fused with structure and subcellular localization.

Ab initio RNA 3D structure prediction from a single sequence, using a composite-likelihood language model and a denoising end-to-end structure module.

Bacterial protein-compound binding affinity prediction from amino acid sequence and SMILES, evaluated zero-shot on two species held out of training.

Tumor microenvironment segmentation on H&E slides, labeling 13 tissue and cell components from a single model in semantic or panoptic form.